plot-section-method: Plot a section Object
In oce: Analysis of Oceanographic Data

plot,section-method

R Documentation

Plot a section Object

Description

Creates a summary plot for a CTD section, with one panel for each value of which.

Usage

## S4 method for signature 'section'
plot(
  x,
  which = c(1, 2, 3, 99),
  eos,
  at = NULL,
  labels = TRUE,
  grid = FALSE,
  contourLevels = NULL,
  contourLabels = NULL,
  stationIndices,
  coastline = "best",
  colLand = "gray",
  xlim = NULL,
  ylim = NULL,
  zlim = NULL,
  zbreaks = NULL,
  zcol = NULL,
  map.xlim = NULL,
  map.ylim = NULL,
  clongitude,
  clatitude,
  span,
  projection = NULL,
  xtype = "distance",
  ytype = "depth",
  ztype = "contour",
  longitude0,
  latitude0,
  legend.loc = "bottomright",
  legend.text = NULL,
  showStations = FALSE,
  showStart = TRUE,
  stationTicks = TRUE,
  showBottom = TRUE,
  showSpine = TRUE,
  drawPalette = TRUE,
  axes = TRUE,
  mgp,
  mar,
  col,
  cex,
  pch,
  lwd,
  labcex = par("cex"),
  debug = getOption("oceDebug"),
  ...
)

Arguments

`x`	a section object.
`which`	a list of desired plot types, as explained in “Details”. There may be up to four panels in total, and the desired plots are placed in these panels, in reading order. If only one panel is plotted, `par` is not adjusted, which makes it easy to add to the plot with subsequent plotting commands.
`eos`	Character indication of the seawater equation of state to use. The permitted choices are `"gsw"` and `"unesco"`. If `eos` is not supplied, it defaults to `getOption⁠("oceEOS",default="gsw")⁠`.
`at`	If `NULL` (the default), the x axis will indicate the distance of the stations from the first in the section. (This may give errors in the contouring routine, if the stations are not present in a geographical order.) If a list, then it indicates the values at which stations will be plotted.
`labels`	Either a logical, indicating whether to put labels on the x axis, or a vector that is a list of labels to be placed at the x positions indicated by `at`.
`grid`	If `TRUE`, points are drawn at data locations.
`contourLevels`	Optional contour levels.
`contourLabels`	Optional contour labels.
`stationIndices`	Optional list of the indices of stations to use. Note that an index is not a station number, e.g. to show the first 4 stations, use `station.indices=1:4`.
`coastline`	Either a coastline object to be used, or a string. In the second case, the permitted choices are `"best"` (the default) to pick a variant that suits the scale, `"coastlineWorld"` for the coarse version that is provided by oce, `"coastlineWorldMedium"` or `"coastlineWorldFine"` for two coastlines provided by the ocedata package, or `"none"`, to avoid drawing a coastline.
`colLand`	colour used to fill in land areas if `which` is `"map"`; ignored otherwise.
`xlim`	Optional limit for x axis (only in sections, not map).
`ylim`	Optional limit for y axis (only in sections, not map)
`zlim, zbreaks, zcol`	Elements that control colours for `image` and `points` plot types, i.e. if `ztype` is either `"points"` or `"image"`. `zlim` is a two-element numerical vector specifying the limit on the plotted field. If not provided, it defaults to the data range. `zbreaks` controls the colour breaks, in a manner that is similar to the `image()` parameter named `breaks`. If not provided, `zbreaks` is inferred from `zlim`. `zcol`, which controls the colour scheme, may be a vector of colours (of length 1 less than `zbreaks`), or a function that takes an integer as its sole argument and returns that number of colours. If not provided, `zcol` defaults to `oceColorsViridis()`. These three parameters are used in Example 6, an illustration of Atlantic salinity along 36N.
`map.xlim, map.ylim`	Optional limits for station map; `map.ylim` is ignored if `map.xlim` is provided.
`clongitude, clatitude, span`	Optional map centre position and span (km).
`projection`	Parameter specifying map projection; see `mapPlot()`. If `projection="automatic"`, however, a projection is devised from the data, with `stereographic` if the mean latitude exceeds 70N and `mollweide` otherwise.
`xtype`	Type of x axis, for contour plots, either `"distance"` for distance (in km) to the first point in the section, `"track"` for distance along the cruise track, `"longitude"`, `"latitude"`, `"time"` or `"spine"` (distance along a spine that was added with `addSpine()`). Note that if the x values are not in order, they will be put in order, and since that might not make physical sense, a warning will be issued.
`ytype`	Type of y axis for contour plots, either `"pressure"` for pressure (in dbar, with zero at the surface) or `"depth"` for depth (in m below the surface, calculated from pressure with `swDepth()`).
`ztype`	String indicating whether to how to indicate the "z" data (in the R sense, i.e. this could be salinity, temperature, etc; it does not mean the vertical coordinate) The choices are: `"contour"` for contours, `"image"` for an image (drawn with `imagep()` with `filledContours=TRUE`), or `"points"` to draw points. In the first two cases, the data must be gridded, with identical pressures at each station.
`longitude0, latitude0`	Location of the point from which distance is measured. These values are ignored unless `xtype` is `"distance"`.
`legend.loc`	Location of legend, as supplied to `legend()`, or set to the empty string to avoid plotting a legend.
`legend.text`	character value indicating the text for the legend. If this is NULL (the default) then the legend is automatically constructed by `labelWithUnit()`, based on the value of `which`.
`showStations`	Logical indicating whether to draw station numbers on maps.
`showStart`	Logical indicating whether to indicate the first station with
`stationTicks`	A logical value indicating whether to indicate station locations with ticks at the top margin of cross-section plots. Setting this parameter to `FALSE` frees the user up to do their own labelling at this spot.
`showBottom`	a value indicating whether (and how) to indicate the ocean bottom on cross-section views. There are three possibilities. (a) If `showBottom` is `FALSE`, then the bottom is not rendered. If it is `TRUE`, then the bottom is rendered with a gray polygon. (b) If `showBottom` is the character value `"polygon"`, then a polygon is drawn, and similarly lines are drawn for `"lines"`, and points for `"points"`. (c) If `showBottom` is a topo object, then the station locations are interpolated to that topography and the results are shown with a polygon. See “Examples”.
`showSpine`	logical value used if `which="map"`. If `showSpine` is `TRUE` and `section` has had a spine added with `addSpine()`, then the spine is drawn in blue.
`drawPalette`	logical value indicating whether to draw a palette when `ztype="image"` ignored otherwise.
`axes`	Logical value indicating whether to draw axes.
`mgp`	A 3-element numerical vector to use for `par(mgp)`, and also for `par(mar)`, computed from this. If not provided, this defaults to `getOption("oceMgp")`.
`mar`	Value to be used with `par("mar")`. If not provided, a default is set up.
`col`	Color for line types. If not provided, this defaults to `par("col")`. See `zcol`, for `ztype="image"` and `ztype="points"`.
`cex`	Numerical character-expansion factor, which defaults to `par("cex")`.
`pch`	Indication of symbol type; defaults to `par("pch")` for non-map or to 3 for map.
`lwd`	line width; defaults to `par("lwd")`.
`labcex`	Size of characters in contour labels (passed to `contour()`).
`debug`	an integer specifying whether debugging information is to be printed during the processing. This is a general parameter that is used by many `oce` functions. Generally, setting `debug=0` turns off the printing, while higher values suggest that more information be printed. If `debug` is not supplied, it defaults to `getOption("oceDebug")`.
`...`	Optional arguments passed to the contouring function.

Details

The type of plot is governed by which, as follows.

which=0 or "potential temperature" for potential temperature contours
which=1 or "temperature" for in-situ temperature contours (the default)
which=2 or "salinity" for salinity contours
which=3 or "sigmaTheta" for sigma-theta contours
which=4 or "nitrate" for nitrate concentration contours
which=5 or "nitrite" for nitrite concentration contours
which=6 or "oxygen" for oxygen concentration contours
which=7 or "phosphate" for phosphate concentration contours
which=8 or "silicate" for silicate concentration contours
which=9 or "u" for eastward velocity
which=10 or "uz" for vertical derivative of eastward velocity
which=11 or "v" for northward velocity
which=12 or "vz" for vertical derivative of northward velocity
which=20 or "data" for a dot for each data location
which=99 or "map" for a location map

The y-axis for the contours is pressure, plotted in the conventional reversed form, so that the water surface appears at the top of the plot. The x-axis is more complicated. If at is not supplied, then the routine calculates x as the distance between the first station in the section and each of the other stations. (This will produce an error if the stations are not ordered geographically, because the contour() routine cannot handle non-increasing axis coordinates.) If at is specified, then it is taken to be the location, in arbitrary units, along the x-axis of labels specified by labels; the way this works is designed to be the same as for axis().

Value

If the original section was gridded, the return value is that section. Otherwise, the gridded section that was constructed for the plot is returned. In both cases, the value is returned silently. The purpose of returning the section is to enable subsequent processing of the grid, including adding elements to the plot (see example 5).

Ancillary Examples

The following examples were once part of the “Examples” section, but were moved here in May 2022, to reduce the build-check time for CRAN submission.

library(oce)
data(section)
GS <- subset(section, 113<=stationId&stationId<=129)
GSg <- sectionGrid(GS, p=seq(0, 2000, 100))

# Gulf Stream, salinity data and contoured
par(mfrow=c(2, 1))
plot(GS, which=1, ylim=c(2000, 0), ztype="points",
     zbreaks=seq(0,30,2), pch=20, cex=3)
plot(GSg, which=1, ztype="image", zbreaks=seq(0,30,2))

# Gulf Stream, temperature grid (image) and data (dots)
par(mfrow=c(1, 1))
plot(GSg, which=1, ztype="image")
T <- GS[["temperature"]]
col <- oceColorsViridis(100)[rescale(T, rlow=1, rhigh=100)]
points(GS[["distance"]],GS[["depth"]],pch=20,cex=3,col="white")
points(GS[["distance"]],GS[["depth"]],pch=20,cex=2.5,col=col)

# 4. Image of temperature, with a high-salinity contour on top;
#    note the Mediterranean water.
sec <- plot(section, which="temperature", ztype="image")
S <- sec[["salinity", "grid:distance-pressure"]]
contour(S$distance, S$pressure, S$field, level=35.8, lwd=3, add=TRUE)

# 5. Contours of salinity, with dots for high pressure and spice
plot(section, which="salinity")
distance <- section[["distance"]]
depth <- section[["depth"]]
spice <- section[["spice"]]
look <- spice > 1.8 & depth > 500
points(distance[look], depth[look], col="red")

# Image of Absolute Salinity, with 4-minute bathymetry
# It's easy to calculate the desired area for the bathymetry,
# but for brevity we'll hard-code it. Note that download.topo()
# requires the "ncdf4" package to have been installed.
if (requireNamespace("ncdf4")) {
    f <- download.topo(west=-80, east=0, south=35, north=40, resolution=4)
    t <- read.topo(f)
    plot(section, which="SA", xtype="longitude", ztype="image", showBottom=t)
}

# Temperature with salinity added in red
plot(GSg, which="temperature")
distance <- GSg[["distance", "byStation"]]
depth <- GSg[["station", 1]][["depth"]]
S <- matrix(GSg[["salinity"]], byrow=TRUE, nrow=length(GSg[["station"]]))
contour(distance, depth, S, col=2, add=TRUE)

# Image with controlled colours
plot(GSg, which="salinity", ztype="image",
    zlim=c(35, 37.5),
    zbreaks=seq(35, 37.5, 0.25),
    zcol=oceColorsTurbo)

Author(s)

Dan Kelley, with help from Clark Richards and Chantelle Layton.

Examples

library(oce)
data(section)
GS <- subset(section, 113<=stationId&stationId<=129)
GSg <- sectionGrid(GS, p=seq(0, 2000, 100))

# Gulf Stream, salinity and temperature contours
plot(GSg, which=c("salinity", "temperature"))

# Gulf Stream, Temperature image
plot(GSg, which="temperature", ztype="image",
    zbreaks=seq(0,25,2), zcol=oceColorsTemperature)

oce documentation built on July 9, 2023, 5:18 p.m.